www.youtube.com/watch?v=6DxlkxA82FM COVID-19 Symposium: Entry of Coronavirus into Cells | Dr. Paul Bates
Amazing talk by Richard Feynman that describes his experiences at Los Alamos National Laboratory while developing the first nuclear weapons.
Transcript: calteches.library.caltech.edu/34/3/FeynmanLosAlamos.htm Also included full text into Surely You're Joking, Mr. Feynman.
- www.youtube.com/watch?v=uY-u1qyRM5w&t=2881s describes the computing aspects. Particularly interesting is the quote about how they used the typist secretary pool to emulate the IBM machines and debug their programs before the machines had arrived. This is exactly analogous to what is done in 2020 in the semiconductor industry, where slower models are used to estimate how future algorithms will run in future hardware.
Los Alamos From Below by Richard Feynman (1975)
Source. Some are named after the encoded protein. Others that are not as clean are just orfXXX for open reading frame XXX.
Spike.
Nucleocapsid phosphoprotein, sticks to the RNA inside.
www.nature.com/articles/s41467-020-20768-y mentions functions:
These are also required for test tube replication.
Microwave only found applications into the 1940s and 1950s, much later than radio, because good enough sources were harder to develop.
One notable development was the cavity magnetron in 1940, which was the basis for the original radar systems of World War II.
E. Coli starts DNA replication before the previous one finished by 
Ciro Santilli 40 Updated 2025-07-16
Ciro Santilli 40 Updated 2025-07-16Run output is placed under
out/:Some of the output data is stored as
.cpickle files. To observe those files, you need the original Python classes, and therefore you have to be inside Docker, from the host it won't work.We can list all the plots that have been produced under Plots are also available in SVG and PDF formats, e.g.:
out/ withfind -name '*.png'The output directory has a hierarchical structure of type:where:
./out/manual/wildtype_000000/000000/generation_000000/000000/wildtype_000000: variant conditions.wildtypeis a human readable label, and000000is an index amongst the possiblewildtypeconditions. For example, we can have different simulations with different nutrients, or different DNA sequences. An example of this is shown at run variants.000000: initial random seed for the initial cell, likely fed to NumPy'snp.random.seedgenereation_000000: this will increase with generations if we simulate multiple cells, which is supported by the model000000: this will presumably contain the cell index within a generation
We also understand that some of the top level directories contain summaries over all cells, e.g. the
massFractionSummary.pdf plot exists at several levels of the hierarchy:./out/manual/plotOut/massFractionSummary.pdf
./out/manual/wildtype_000000/plotOut/massFractionSummary.pdf
./out/manual/wildtype_000000/000000/plotOut/massFractionSummary.pdf
./out/manual/wildtype_000000/000000/generation_000000/000000/plotOut/massFractionSummary.pdfEach of thoes four levels of
plotOut is generated by a different one of the analysis scripts:./out/manual/plotOut: generated bypython runscripts/manual/analysisVariant.py. Contains comparisons of different variant conditions. We confirm this by looking at the results of run variants../out/manual/wildtype_000000/plotOut: generated bypython runscripts/manual/analysisCohort.py --variant_index 0. TODO not sure how to differentiate between two different labels e.g.wildtype_000000andsomethingElse_000000. If-vis not given, a it just picks the first one alphabetically. TODO not sure how to automatically generate all of those plots without inspecting the directories../out/manual/wildtype_000000/000000/plotOut: generated bypython runscripts/manual/analysisMultigen.py --variant_index 0 --seed 0./out/manual/wildtype_000000/000000/generation_000000/000000/plotOut: generated bypython runscripts/manual/analysisSingle.py --variant_index 0 --seed 0 --generation 0 --daughter 0. Contains information about a single specific cell.
Gospel of Matthew 4 King James Version:
18 And Jesus, walking by the sea of Galilee, saw two brethren, Simon called Peter, and andrew the Apostle his brother, casting a net into the sea: for they were fishers.19 And he saith unto them, Follow me, and I will make you fishers of men.
It would be boring if we could only simulate the same condition all the time, so let's have a look at the different boundary conditions that we can apply to the cell!
We are able to alter things like the composition of the external medium, and the genome of the bacteria, which will make the bacteria behave differently.
The variant selection is a bit cumbersome as we have to use indexes instead of names, but one you know what you are doing, it is fine.
Of course, genetic modification is limited only to experimentally known protein interactions due to the intractability of computational protein folding and computational chemistry in general, solving those would bsai.
The default run variant, if you don't pass any options, just has the minimal growth conditions set. What this means can be seen at condition.
Notably, this implies a growth medium that includes glucose and salt. It also includes oxygen, which is not strictly required, but greatly benefits cell growth, and is of course easier to have than not have as it is part of the atmosphere!
But the medium does not include amino acids, which the bacteria will have to produce by itself.
Pinned article: Introduction to the OurBigBook Project
Welcome to the OurBigBook Project! Our goal is to create the perfect publishing platform for STEM subjects, and get university-level students to write the best free STEM tutorials ever.
Everyone is welcome to create an account and play with the site: ourbigbook.com/go/register. We belive that students themselves can write amazing tutorials, but teachers are welcome too. You can write about anything you want, it doesn't have to be STEM or even educational. Silly test content is very welcome and you won't be penalized in any way. Just keep it legal!
Intro to OurBigBook
. Source. We have two killer features:
- topics: topics group articles by different users with the same title, e.g. here is the topic for the "Fundamental Theorem of Calculus" ourbigbook.com/go/topic/fundamental-theorem-of-calculusArticles of different users are sorted by upvote within each article page. This feature is a bit like:
- a Wikipedia where each user can have their own version of each article
- a Q&A website like Stack Overflow, where multiple people can give their views on a given topic, and the best ones are sorted by upvote. Except you don't need to wait for someone to ask first, and any topic goes, no matter how narrow or broad
This feature makes it possible for readers to find better explanations of any topic created by other writers. And it allows writers to create an explanation in a place that readers might actually find it.
Figure 1. Screenshot of the "Derivative" topic page. View it live at: ourbigbook.com/go/topic/derivativeVideo 2. OurBigBook Web topics demo. Source. - local editing: you can store all your personal knowledge base content locally in a plaintext markup format that can be edited locally and published either:This way you can be sure that even if OurBigBook.com were to go down one day (which we have no plans to do as it is quite cheap to host!), your content will still be perfectly readable as a static site.
- to OurBigBook.com to get awesome multi-user features like topics and likes
- as HTML files to a static website, which you can host yourself for free on many external providers like GitHub Pages, and remain in full control
Figure 3. Visual Studio Code extension installation.
Figure 4. Visual Studio Code extension tree navigation.
Figure 5. Web editor. You can also edit articles on the Web editor without installing anything locally.Video 3. Edit locally and publish demo. Source. This shows editing OurBigBook Markup and publishing it using the Visual Studio Code extension.Video 4. OurBigBook Visual Studio Code extension editing and navigation demo. Source. 
- Infinitely deep tables of contents:
All our software is open source and hosted at: github.com/ourbigbook/ourbigbook
Further documentation can be found at: docs.ourbigbook.com
Feel free to reach our to us for any help or suggestions: docs.ourbigbook.com/#contact